2R0J

Crystal structure of the putative ubiquitin conjugating enzyme, PFE1350c, from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QCQPDB entry 1QCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62983.5M Sodium formate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1560.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.747α = 90
b = 73.747β = 90
c = 79.112γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.855099.70.0470.0420.613.81922419224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9299.40.5670.6271.613.61860

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QCQ1.8532.99192031920398599.710.1950.1950.1930.231RANDOM32.088
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.090.09-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.584
r_dihedral_angle_4_deg16.987
r_dihedral_angle_3_deg14.685
r_dihedral_angle_1_deg6.632
r_scangle_it6.202
r_scbond_it4.365
r_mcangle_it2.79
r_angle_refined_deg2.313
r_mcbond_it2.081
r_symmetry_hbond_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.584
r_dihedral_angle_4_deg16.987
r_dihedral_angle_3_deg14.685
r_dihedral_angle_1_deg6.632
r_scangle_it6.202
r_scbond_it4.365
r_mcangle_it2.79
r_angle_refined_deg2.313
r_mcbond_it2.081
r_symmetry_hbond_refined0.321
r_nbtor_refined0.313
r_nbd_refined0.221
r_xyhbond_nbd_refined0.216
r_symmetry_vdw_refined0.193
r_chiral_restr0.191
r_bond_refined_d0.033
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1185
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction